Hi Kim,
we do have some tools for smoothing the hippocampal surfaces, but we
haven't distributed them. I could try to get you a beta version if you
like.
cheers,
Bruce
On Fri, 16 Nov 2007, Kim Mouridsen wrote:
Hi Nick,
The Freesurfer version I use has build stamp
freesurfer-Darwin-tiger-i686-stable-pub-v4.0.1
After conversion, read_asc.m doesn't work - seemingly due to a
dimension problem. In the code I see that 5 elements are expected for
faces and indicies, whereas only 4 elements are provided in the .asc
file. I changed lines 45-46 into
f = fscanf(fp, '%d', S(3)*4);
f = reshape(f, [4 S(3)])';
Using patch in Matlab with v(:,1:3) as vertices and f(:,[1 3 2]) as
faces, I get an image of the hippocampus surface.
The surface looks good(!) but is a bit rough and 'spiky'. Is this
because the segmentation procedure does not employ a smoothness
constraint?
The aim of all this is to prepare hippocampal volumes for deformation
analysis (two groups, two time points). Is the following line of
processing appropriate:
Topology correction:
mri_topologycorrection -label "hippocampus" subject/mri/norm.mgz
subject/mri/aseg.mgz aseg_corrected
Tesselate surface:
mri_tessellate
Smooth surface:
mris_smooth
Convert to ascii for use with Matlab:
mris_convert
Cheers!
Kim.
2007/11/16, Nick Schmansky <[EMAIL PROTECTED]>:
Kim,
Which version of freesurfer is being used?
An alternative approach is to convert the surface to ascii:
mris_convert surface_file surface_file.asc
where the .asc extension is an output ascii file listing the vertices
and faces.
Nick
On Thu, 2007-11-15 at 16:18 +0100, Kim Mouridsen wrote:
Hi,
We have segmented hippocampus using Freesurfer, and want to generate a
surface which can be read into matlab.
We use mri_tesselate and mris_smooth. However, the resulting file can
not be read into matlab using read_surf. The error we get is
??? Undefined function or variable "vertex_coords".
Error in ==> read_surf at 77
vertex_coords = reshape(vertex_coords, 3, vnum)' ;
It seems the 'magic' number is 16777213, whereas only 16777214 and
16777215 are supported in read_surf.m
How can we read the result of mris_smooth into matlab?
Thanks!
Kim.
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